Remembering COVID: Atlas Genomics Detects UK Coronavirus Variant with PCR Test, Result Confirmed with RNA Sequencing

Editor’s Note: On May 11, 2023, the World Health Organization officially ended the global COVID-19 Public Health Emergency. While much of the world has since moved on, healthcare professionals, particularly those in medical laboratory operations and laboratory information systems (LIS systems) development, must continue to reflect on the critical lessons learned and stay prepared for future infectious disease threats.

Learn More: End of the Federal COVID-19 Public Health Emergency (PHE) Declaration

At LigoLab, our top priority throughout the pandemic was supporting our laboratory partners. We quickly adapted to their evolving needs with advanced LIS software and direct-to-consumer lab testing solutions designed to overcome unique challenges brought on by the crisis. We streamlined laboratory workflow management, safeguarded patient care, and built resilient diagnostic lab software systems under extraordinary pressure.

One of the most powerful parts of this experience was witnessing the determination and adaptability of our lab partners. As we continue to honor their commitment, we are reminded of a pivotal moment from February 2021 - a reminder of COVID-19’s lasting impact and the vital role that modern LIS pathology technology will continue to play in public health readiness.

Atlas Genomics’ Use of Advanced PCR Testing and LigoLab LIS System Platform Support

LOS ANGELES, CA – A new mutation of COVID-19 that shows increased transmissibility was recently detected in the Seattle metro area with a PCR (polymerase chain reaction) test. The variant, which first emerged in the United Kingdom before spreading to other countries, was later confirmed with RNA sequencing by the University of Washington Department of Laboratory Medicine and Pathology as the UK coronavirus variant called B.1.1.7.

The B.1.1.7 variant, the first of its kind discovered in King County, was detected by Atlas Genomics, a high-complexity, molecular diagnostics laboratory that serves Washington state with high-volume public COVID testing sites in Renton, Tacoma (at Cheney Stadium), Chelan, and Douglas counties. Atlas Genomics, supported by LigoLab’s all-in-one medical LIS & lab RCM informatics platform, detected the mutation using a three-target assay.

Case Study: Remembering COVID - A Medical Lab’s Journey to One Million COVID-19 Tests

According to Atlas’ Medical Director, Dr. Michael H. Kalnoski, the B.1.1.7 variant has a small deletion in its genome, which causes the S gene (responsible for making the Spike protein) - one of the three assay targets - to go undetected by the COVID PCR test. If the S gene “drops out” and the other two targets are positive, this may indicate the presence of the UK coronavirus variant.

Lab officials also said the ability to detect the UK variant with a PCR test was good news because that means patients and public health officials can be notified about the potential mutation in a matter of hours. Sequencing would still be required to confirm the suspected variant, but obtaining PCR results expeditiously is helpful.

“Speed is critical when dealing with a variant shown to be more contagious,” said Atlas Genomics General Manager Rob Rovig. “If our test can pick it up with PCR, then we’ll know well within 24 hours rather than waiting a week or longer to get the variant confirmed through RNA sequencing.”

Atlas Genomics is one of dozens of laboratories using LigoLab’s direct-to-consumer lab testing solution called TestDirectly, a web-based molecular lab testing software and patient engagement portal that removes paper forms, creates a digital workflow, and improves turnaround times while connecting patients directly with the laboratories for test results. 

In this case, with TestDirectly (TestDirectly.com), the patient and public health officials were automatically notified about the positive result in real-time, enabling the patient to quarantine immediately and mitigate disease spread.  

TestDirectly Streamlines COVID-19 Testing and Reporting with a Patient-Friendly, End-to-End Molecular LIS Solution

According to LigoLab CEO Suren Avunjian, TestDirectly was developed as a light-weight molecular LIS solution to remove potential delays in the laboratory and facilitate safe and streamlined COVID-19 testing.

“With more testing and fast and accurate TestDirectly results, we can identify the virus and its mutations, take action to contain its spread, and start making our way toward a more normal life,” said Avunjian. “With the new variants, we encourage the public to stay vigilant. The vaccines are here, but it will be months before the average person can get vaccinated.”

Avunjian said getting vaccinated is part of the solution, as is getting tested, wearing a mask, avoiding crowds, and regular handwashing.

TestDirectly is a lab pathology software that eliminates paperwork and manual processes, enabling patients to self-register, select a local collection facility, and book an appointment - all from the comfort of their computer or mobile device. 

The platform supports community and organizational testing, drive-through, walk-up, and on-site collection workflows, while covering the entire life cycle of a case and a specimen, including laboratory processing, report delivery via email or SMS, and laboratory billing (lab revenue cycle management) operations.

‍Learn More: Molecular LIS Labs Hold the Key to Evidence-Based Precision Medicine

About TestDirectly

TestDirectly is a web-based direct-to-consumer lab testing portal that works seamlessly with laboratory information systems (LIS software), Electronic Health Record (EHR) systems, and billing software for labs to replace paper requisitions and the need for manual order entry with a streamlined electronic workflow that boosts testing capacity and improves turnaround times. The portal supports a case and a specimen throughout the testing journey, including patient self-registration and appointment scheduling, specimen collection, laboratory processing, report delivery, and laboratory billing operations.

‍About LigoLab

LigoLab is a leading provider of innovative end-to-end healthcare LIS software, servicing 300+ facilities nationwide. As a comprehensive enterprise-grade pathology software solution, the LigoLab medical LIS & lab RCM informatics platform™ includes all modules and engines a modern, full-service clinical laboratory could ever need, all integrated to support the entire life cycle of all cases, enabling laboratories to differentiate themselves in the marketplace, scale their operations, and become more profitable.

‍About Atlas Genomics

Atlas Genomics is a high-complexity, CLIA-certified molecular diagnostic laboratory in Seattle, Washington. Atlas Genomics offers PCR testing for COVID-19 and next-generation sequencing technology to assist in the confirmation of potential COVID-19 variants. Atlas provides testing services for multiple public COVID testing sites, working with state and local health jurisdictions while supporting businesses for “return to work” programs that monitor workplaces for COVID-19.